June 29, 2005

Spencer Wells reveals that Thomas Jefferson, one of the "founding fathers" of the United States belonged to Y-chromosome haplogroup K2:

"As part of our genetic analyses for the film SEARCH FOR ADAM, we analyzed additional markers on Jefferson's Y-chromosome in an effort to determine why it is so unusual. If you recall the original Hemmings paper in Nature by Foster et al., the haplotype was 'rare', which is what enabled them to implicate Jefferson as the source rather than another European. At the time there were no matches among the 607 European men (Jefferson's father claimed Welsh ancestry) who had been genotyped for the same 11 microsatellites. Recent searches of more comprehensive databases have turned up related haplotypes belonging to haplogroups O, K and Q. We investigated the 12 microsatellites routinely typed by FTDNA, which did not add to the haplogroup resolution. SNP testing, however, revealed that Jefferson's Y is positive for M70, which places him in haplogroup K2. K2 is rare in northern Europe (only one K was found among 1772 British men surveyed by Capelli et al., but it wasn't typed for M70) but quite common in the Middle East and northeast Africa, where it reaches frequencies of 10% or more. Interestingly, another person typed in the film, the Ethiopian prince, is also K2, but many mutational steps removed from Jefferson. We are currently looking at potential source populations for Jefferson's K2 as part of a broader survey of Y-chromosome variation in the Middle East and North Africa, and expect to submit a publication by the end of the year. I'm sure that all of you will appreciate the amount of effort that has gone into launching The Genographic Project, and hope that you will understand that our publication schedule has been somewhat delayed as a result.

Spencer WellsMission ProgramsNational Geographic Society"

Some information on Y-haplogroup K2 and its presence in human populations: onetwothree.

UPDATE:

According to this paper (pdf), K2 is found at substantial frequencies in various Spanish populations. The simplest explanation for its presence in Thomas Jefferson might be that he was the descendant of a Spaniard.

A new paper analyzes the occurrence of mtDNA of African (North or Sub-Saharan) origin in the Iberian peninsula. The following snippet is also interesting because it quantifies the Sub-Saharan African admixture in the rest of Europe:

The pattern of L sequences in Iberia is different from the pattern observed in the rest of Europe, where just a few instances were observed, even in countries also involved in the slave trade. Indeed, a general survey of the literature on Europeans provided the following cases of sub-Saharan sequences: one L1b (16126-16175-16189-16223-16264-16270-16278-16311) in 161 German-Danish (Richards et al. 1996); one L1c (16129-16189-16223-16278-16284-16294-16311-16360) in 100 British (Piercy et al. 1993); one L1a (16086-16129-16148-16166-16168-16172-16187-16188C/G-16189-16223-16230-16311-16320) in 42 Albanians (Belledi et al. 2000); one L3 (16189-16223-16291C/A) in 50 Finnish (Sajantila et al. 1995); one L1a1 (16129-16148-16168-16172-16187-16188C/G-16189-16223-16230-16311-16320) and one L2a (16093-16189-16192-16223-16278-16294) in 69 Sardinians (Di Rienzo and Wilson 1991); and one L2a (16145-16189-16192-16223-16278-16294-16309-16390) in 106 Sicilians (Cali et al. 2001).

Human Biology 77.2 (2005) 213-229

African Female Heritage in Iberia:A Reassessment of mtDNA Lineage Distribution in Present Times

Luísa Pereira et al.

Abstract

The Iberian peninsula is a peripheral region of Europe in close proximity to Africa. Its inhabitants have an overall mtDNA genetic landscape typical of European background, although with signs of some African influence, whose features we deemed to disclose by analyzing available mtDNA HVRI distributions and new data. We analyzed 1,045 sequences. The most relevant results are the following: (1) North African sequences (haplogroup U6) present an overall frequency of 2.39%, and sub-Saharan sequences reach 3.83%, values that are, in both cases, much higher than those generally observed in Europe; and (2) there is a substantial geographic heterogeneity in the distribution of these lineages (haplogroup L being the most frequent in the south, whereas haplogroup U6 is generally more common in the north). The analysis of the observed diversity within each haplogroup strongly suggests that both were recently introduced (in historical times). Although for haplogroup U6 the documented event that is demographically compatible is the Islamic period (beginning of the 8th century to the end of the 15th century), for haplogroup L the most probable origin is the modern slave trade (mid 15th century to the end of the 18th century). However, the observed geographic structuring for one of the haplogroups does not fit the expected distribution provided by simplistic historical considerations. In fact, although for haplogroup L the north-south increasing frequency is corroborated by historical data, the opposite trend, observed for haplogroup U6, is more difficult to reconcile with the magnitude and time span of the Islamic political and cultural influence, which lasted longer and was more intense in the south. To clarify this conundrum, we need not only a substantial increase in the amount of mtDNA data (particularly for North Africa) but also new historical data and interpretations.

This is the third paper on the subject that has appeared over the last year. The othertwo. The "Jewish" connection is derived mainly from historical data, as only haplogroup J was typed, and not its subhaplogroups or any microsatellites.

Peopling of the Azores Islands (Portugal):Data from the Y Chromosome

Olga Fernando et al.

Abstract

Nine Atlantic islands with approximately five and a half centuries of demographic history constitute the Portuguese archipelago of the Azores. Despite the recent peopling history of these islands, written records regarding the specific origin and relative proportions of the first settlers are scarce and incomplete. To gain insights into the history of the peopling of the Azores and to evaluate to what extent population imports described in historical sources left their marks on the genetic constitution of the present-day populations, we analyzed 11 Y-chromosome biallelic markers in a sample of 145 unrelated individuals of Azorean ancestry. The main results of this study indicate that the genetic profile of the Azorean male population shows high affinities with that of mainland Portugal, in accordance with the general knowledge, derived from historical sources, that the Portuguese were the major contributors to the Azorean founding population. Nevertheless, genetic traces of settlers from other origins also mentioned in historical records can still be found in the present-day population. Thus typically sub-Saharan male lineages were detected in the archipelago, in contrast to what has been described for mainland Portugal. Furthermore, compared to what has been described for the mainland Portugal population, our data support a stronger influence of people of Jewish origin, as detected by an increased frequency of lineages belonging to haplogroup J.

This paper argues that Polynesians may have originated later than previously thought.

Human Biology 77.2 (2005) 179-188

Indonesian Mitochondrial DNA and Its Opposition to a Pleistocene Era Origin of Proto-Polynesians in Island Southeast Asia

Murray P. Cox

Abstract

The origin of modern Polynesians, the route of their expansion into the Pacific Ocean, and the timing of their movements all remain contentious topics in modern anthropology. Numerous studies have used molecular data to elucidate settlement patterns in the Indo-Pacific region, but the same evidence is often interpreted in opposing ways by different researchers. Above all, mitochondrial DNA (mtDNA) diversity has been used to discriminate between competing migration models and has narrowed the probable source of proto-Polynesian peoples to southern China and Taiwan or eastern Indonesia. Richards et al. (1998) used a dating method employing the ρ statistic to argue for an origin of Polynesian peoples in eastern Indonesia during the Pleistocene (>10,000 years ago). Here, the time to the most recent common ancestor (TMRCA) is recalculated for a new series of Indonesian mtDNA sequences with Polynesian affinities. These data, which incorporate additional sequences published after 1998, produce dates that cannot rule out the possibility of a common ancestor for these sequences during the Holocene (<10,000>This implies that previous estimates of TMRCA dates for Indonesian sequences lacked the statistical robustness necessary for replicability. The extant mtDNA evidence can no longer be viewed as favoring a Polynesian origin in eastern Indonesia, but instead remains consistent with an origin of proto-Polynesian peoples in southern China and Taiwan.

Interesting paper on Maori origins. The "slow boat" model referred to in the abstract is explained as follows:

A third model, the "slow boat" model (Richards et al. 1998; Lum and Cann 1998, 2000; Oppenheimer and Richards 2001a, 2001b), combines elements from the other two models, allowing genetic input into the ancestors of Polynesians from both "Melanesian" Papuan speakers (after the entangled bank model) and Austronesian speakers from east and southeast Asia (express train model). In addition, it attributes the general origin of the expansion to somewhere within island Southeast Asia and does not rule out Taiwan.

Human Biology 77.2 (2005) 157-177

Human Evolution in Polynesia

Adele L. H. Whyte et al.

Abstract

The number of eastern Polynesian females required to found the Māori population of Aotearoa (New Zealand) has been recalculated. Our estimates use computer simulations that incorporate realistic sigmoid population growth models and include previously published and new mitochondrial DNA (mtDNA) 3' hypervariable region 1 sequences from Māori (N = 109) and other eastern Polynesian (N = 125) volunteers. Approximately 190 (170–230) women are estimated to have been present in the founding waka (canoes). This new figure is more than double the previous estimate (Murray-McIntosh et al. 1998). Our claim for a large Māori founding population fits well with Māori oral history and has additional support from Māori paleodemography studies based on fertility estimates (Brewis et al. 1990; Pool 1991). An increasing body of data, including our own, supports the concept of planned multiple settlement voyages to Aotearoa by Polynesian navigators, leading us to suggest that theories for an "accidental discovery" of Aotearoa can now be completely disregarded. Four rare and novel Māori mtDNA haplotypes have been identified in the present study, but we are unable to assign the immediate origin of Māori to an exact Pacific island "homeland" because these haplotypes are not currently known elsewhere in Polynesia. We also discuss briefly the ultimate origin of all Polynesians (including Māori) in a wider context. In general, we support the emerging consensus for Pacific origins most closely encapsulated by the "slow boat" model (Oppenheimer and Richards 2001a). Previously "competing" models for the settlement of Oceania are seen as extremes in a continuum of possibilities with the slow boat representing an "intermediate" model. We suggest that a complete account is now close, incorporating data from all relevant interdisciplinary fields to provide a "synthetic total evidence theory."

Use of short tandem repeats loci to study the genetic structure of several populations from Zulia State, Venezuela

William M. Zabala Fernández et al.

Abstract

Genetic relationships between populations can be studied by comparing genotypic and allelic similarities. This investigation aims to demonstrate that selected autosomal microsatellite markers could be used to study the genetic structures of different populations living in northwest Venezuela, in Zulia State. Seven autosomal systems (CSF1PO, TPOX, TH01, vWA, D7S820, D13S317, and D5S818) were tested by PCR in a multiplex format on 688 different chromosomes from unrelated individuals living in Maracaibo, Isla de Toas, and San José de Heras, and from two Amerindian populations from the Sierra de Perijá, Barí' and Yukpa. Allele frequencies, Hardy-Weinberg equilibria, genetic distances, phylogenetic trees, and ethnic admixtures were estimated. The study shows the existence of a clear genetic difference among these populations in accordance with their historic evolution. The populations of Maracaibo and Isla de Toas showed a triracial origin, with a large European contribution, followed by an Amerindian component and a small African component. The indigenous groups, Barí' and Yukpa, showed exclusively an Amerindian component, and San José de Heras showed only an African component. These results indicate that microsatellite markers are useful for molecular anthropology in a regional and worldwide context and provide important genetic information about contemporary populations of Venezuela.

Heterogeneity of the genome ancestry of individuals classified as White in the State of Rio Grande do Sul, Brazil.

Marrero AR et al.

One hundred nineteen individuals classified as White, living in different localities of the Brazilian state of Rio Grande do Sul, were studied in relation to the HVS-I region of the mitochondrial DNA (mtDNA). The male fraction of the sample (N = 74) was also tested for seven Y-chromosome polymorphisms. In a specific population (Veranopolis), a city characterized by a large influence of the Italian immigration of the 19th century, the results from the maternal and paternal sides indicated almost complete European ancestry. However, another sample identified as White, from different localities of Rio Grande do Sul, presented significant fractions of Native American (36%) and African (16%) mtDNA haplogroups. These results indicate that Brazilian populations are remarkably heterogeneous; while some present an overwhelming majority of transplanted European genomes, with a complete correspondence between physical appearance and ancestry, others reflect a history of extensive admixture with dissociation between physical appearance and ancestry.

June 28, 2005

His latest adventures have led him to discover that Thomas Jefferson’s ethnic background is not quite as one would expect. He has hunted down possible descendents of Solomon, the third king of Israel. And, he has entered a world where science and religion converge—the search for what he calls the “scientific Adam,” the man who gave rise to all men today and the “trunk” of the human family tree. Wells has used DNA to trace this common ancestor back to Africa and perhaps to the very plains where he may have hunted. He has even identified a living tribe with an ancient lineage that offers a window into the life of “scientific Adam”—and, the face of one of the tribe members served as a model to determine what he may have looked like.

According to some people who have watched the TV special, Spencer Wells has indicated that Thomas Jefferson's Y-chromosome was "Phoenician", which probably means that it belongs to one of the haplogroups entering Europe from the Near East in the Neolithic and later. The "Face of Adam", according to Animetrics:

A very interesting article for the genetic composition of Russians as evidence by uniparentally inherited markers. From the Introduction:

The origin of Eastern Slavs (Russians, Ukrainians, and Belorussians) is a complex issue that has been debated by linguists, anthropologists, archeologists, and [End Page 877]historians for more than 300 years. The Slavonic colonization of eastern Europe [which was most intensive in the 6th–7th centuries A.D. according to archeological data (Sedov 1995)] has entailed changes in the anthropological composition of Slavs because of their interpopulation contacts with Baltic tribes in the northwest, Finno-Ugric tribes in the north and east, and Iranian (or Iranic-speaking) tribes in the south of eastern Europe (Alekseeva and Alekseev 1989). Notwithstanding the vast factual material concerning ancient and modern Eastern Slavonic populations, accumulated by archeologists, anthropologists, and historians, many problems still remain unsolved, including the character of interactions between Slavs and autochthonous populations of eastern Europe.

Previous genetic studies of classical genetic markers (Rychkov et al. 1999) and anthropological data (Alekseeva 1973; Rychkov and Balanovska 1988) have shown geographic differences between Russian populations and have allowed researchers to recognize at least two groups of Russians. It has been suggested that the most western Russian populations appear to be descendants of the Slavs, whereas northern, eastern, and southern Russian populations are the result of admixture between Slavonic tribes and pre-Slavonic populations of eastern Europe (Rychkov and Balanovska 1988). In addition, principal components analyses performed on the basis of anthropological data revealed that modern Russians are represented by two regional groups of populations, southeastern and northwestern (Alekseeva 1999). Using computer cartography of anthropological and genetic data, Balanovsky and Balanovska (2002) recently identified a latitudinal (north–south) trend as the main geographic pattern of the Russian gene pool variation.

Some information about Y-chromosome haplogroup N3, which is found at an frequency ranging from 4.5-35%, and is indicative of Finno-Ugric admixture:

It is noteworthy that among the Russian populations studied, the Pskov population shows the highest frequency (35%) of haplogroup N3, which is characteristic of all Uralic- and Baltic-speaking populations north and east of the Baltic Sea (Rosser et al. 2000; Zerjal et al. 2001). This haplogroup is considered a signature of Uralic Finno-Ugric-speaking tribes migrating to northern Europe about 5,000 years ago (Passarino et al. 2002). The presence of haplogroup N3 in Russians suggests that some admixture between Slavonic and Finno-Ugric and/or Baltic tribes occurred during the colonization of the East European plain by Slavs in the early Middle Ages and later. In addition, the distribution pattern of haplogroup N3 in other Slavonic-speaking populations suggests that proto-Slavs probably did not carry this lineage at a substantial frequency (Barac et al. 2003).

Finally, the conclusions of the study:

Y-chromosome variation data obtained in the present study demonstrate that the Russian gene pool appears to be close to central-eastern European populations. The data show a high frequency of haplogroups R1a and N3. The high incidence of R1a haplotypes in Eastern Slavs and in Baltic and some Finno-Ugric populations of eastern Europe is a well-established fact (Rosser et al. 2000; Wells et al. 2001; Zerjal et al. 2001), but little is known about the spread of haplogroup N3 in different Russian populations. Our data indicate that this haplogroup is unevenly distributed in Russian populations, with frequencies ranging from 4.8% to 35%. It is noteworthy that in most of the populations studied (with the exception of the Pskov sample) the frequency of haplogroup N3 does not exceed 20%. An important feature distinguishing Russians from their eastern European neighbors is almost complete absence of paragroup N*, which is ancestral to haplogroup N3. In Europe the highest frequencies of paragroup N* (up to 42.5%) were detected in Volga Finno-Ugric populations: Udmurts and Mari (Rosser et al. 2000; Khusnutdinova et al. 2002). Therefore Y-chromosome data suggest that the Russian male gene pool is characterized by its own structural features, although genetic influences on Russians from Uralic- or Baltic-speaking populations are also highlighted. The latter is clearly defined in the most northern Russian populations, such as Pskov Russians and Pomors. A possible explanation for this phenomenon includes replacement of an earlier Uralic or Baltic language in populations of the north of eastern Europe by the present Russian language, occurring with a low input of Slavonic mtDNA and Y-chromosome haplotypes. The high frequency of haplogroup N3 in Pskov and Pomor Russians (and probably in other northern Russian populations) is striking and should be investigated further using Y-chromosome STR analysis and a comparison with published N3-associated Y-chromosome STR haplotype data in Finno-Ugric and Baltic populations. These data should be studied with respect to the hypothesis that the genetic history of N3 Y chromosomes in Baltic-speaking populations is distinct from that of the Uralic speakers and "that there were two distinct early migrations of haplogroup 16 into Europe" (Zerjal et al. 2001). To test this and other hypotheses concerning the recent historical interactions between eastern European populations, more populations need to be studied for more genetic markers.

The present study demonstrates that Russian populations contain relatively high levels of mtDNA sequence diversity (in the means of pairwise nucleotide [End Page 896] differences), but the level of FST-based between-population differentiation is low. However, the results of the multidimensional scaling analysis performed on the basis of pairwise FST values for mtDNA HVSI sequences suggest that the Russian populations can be differentiated into subregions. The multidimensional scaling analysis revealed that Russian populations analyzed in combination with other central and eastern European populations do not cluster together and that populations from the southern and western parts of Russia (such as Stavropol, Rostov, Kursk, Orel, Kaluga, and Saratov) are separated from eastern and northern populations (Vladimir, Tula, Yaroslavl, Kostroma, and Pskov). Interestingly, southwestern Russian populations demonstrate genetic similarities with a set of central and northern European populations of different linguistic affiliation [Slavonic, Baltic, Germanic, and even Finno-Ugric (Estonians)], whereas northeastern Russian populations cluster together with eastern and northern European populations speaking not only Finno-Ugric languages but also Turkic (Tatars) and North Caucasus (Adygei) ones.

The multidimensional scaling analysis performed on the basis of pairwise FST values for Y-chromosome haplogroup data shows a somewhat different picture (for mtDNA sequences) of population differentiation in Russia. The most important subdivision was found only between northern populations of Pskov and Pomor Russians and the rest of the Russian populations studied. Historically, this observed discrepancy in the depth of penetration of mtDNA and Y-chromosome lineages characteristic for the most southwestern Russian populations into the east and north of eastern Europe may indicate [in accordance with anthropological data (Rychkov and Balanovska 1988)] that only the most western Russian populations appear to be descendants of the Slavs, whereas northern and eastern Russian populations seem to be the result of an admixture between Slavonic tribes and pre-Slavonic populations of eastern Europe. In addition, the data allow one to assume the possibility that Slavonic male lineages penetrated the original eastern European populations further than mtDNA lineages. One should note, however, that this scenario should be tested with additional mtDNA and Y-chromosome data in multiple Russian-, Finno-Ugric-, and Turkic-speaking populations of eastern Europe, which are poorly characterized genetically.

In addition, to estimate the degree of population replacement in eastern Europe associated with the Slavonic colonization starting in the early Middle Ages [6th–7th centuries A.D. according to archeological data (Sedov 1995)], it would be important to perform analyses of multiple samples from small urban areas, because such an approach seems to be informative in genetic history studies (Capelli et al. 2003).

Hum Biol. 2004 Dec;76(6):877-900

Differentiation of mitochondrial DNA and Y chromosomes in Russian populations

Malyarchuk B et al.

The genetic composition of the Russian population was investigated by analyzing both mitochondrial DNA (mtDNA) and Y-chromosome loci polymorphisms that allow for the different components of a population gene pool to be studied, depending on the mode of DNA marker inheritance. mtDNA sequence variation was examined by using hypervariable segment I (HVSI) sequencing and restriction analysis of the haplogroup-specific sites in 325 individuals representing 5 Russian populations from the European part of Russia. The Y-chromosome variation was investigated in 338 individuals from 8 Russian populations (including 5 populations analyzed for mtDNA variation) using 12 binary markers. For both uniparental systems most of the observed haplogroups fell into major West Eurasian haplogroups (97.9% and 99.7% for mtDNA and Y-chromosome haplogroups, respectively). Multidimensional scaling analysis based on pairwise F(ST) values between mtDNA HVSI sequences in Russians compared to other European populations revealed a considerable heterogeneity of Russian populations; populations from the southern and western parts of Russia are separated from eastern and northern populations. Meanwhile, the multidimensional scaling analysis based on Y-chromosome haplogroup F(ST) values demonstrates that the Russian gene pool is close to central-eastern European populations, with a much higher similarity to the Baltic and Finno-Ugric male pools from northern European Russia. This discrepancy in the depth of penetration of mtDNA and Y-chromosome lineages characteristic for the most southwestern Russian populations into the east and north of eastern Europe appears to indicate that Russian colonization of the northeastern territories might have been accomplished mainly by males rather than by females.

June 27, 2005

Whit Athey's haplogroup predictor is a very useful tool for predicting your monophyletic Y-chromosomal lineage (haplogroup) from Y-chromosomal short tandem repeat (STR) data that is usually reported by DNA testing companies. It is also quite useful for inferring the haplogroup of Y-STR haplotypes published in the literature.

Now, the haplogroup predictor has a new updated stable version, as well as a new beta version. This is a great example of how laymen can produce a high quality/high utility product that helps thousands of others; judging from personal experience (sample size=1), Athey's haplogroup predictor is more accurate than that of at least one well-known testing company, and I have yet to receive a bizarre result from it when using it with haplotype data from the literature.

A new series of archaeological discoveries in Britain serves to re-write the history of the Roman arrival in that island. It was previously thought that the Romans invaded and conquered Britain in 43AD. But, the new discoveries attest to their much earlier presence there and their role as liberators against local tribal kings.

The history of Britain will have to be rewritten. The AD43 Roman invasion never happened - and was simply a piece of sophisticated political spin by a weak Emperor Claudius.

A series of astonishing archaeological findings of Roman military equipment, to be revealed this week, will prove that the Romans had already arrived decades earlier - and that they had been welcomed with open arms by ancient Britons.

June 19, 2005

A reader alerts me to an M.Sc. thesis about the human mtDNA haplogroup R in India. This haplogroup branched from haplogroup N very early after the dispersion of humans out of East Africa. The study concludes that haplogroup R lineages in India are easily distinguishable from those of Western Eurasia.

There has been a new release of YHRD which now contains 31,319 haplotypes in a set of 258 populations. I have used YHRD in the past to see the distribution of various interesting haplotypes, and it will be interesting if some of the patterns I identified still hold in the new release.

For example, in Global prevalence of Mongolian and Kazakh modal haplotypes I showed that the modal haplotypes of Mongolians and Kazakhs are quite specific to these populations and absent in the other listed populations, except in a sample of Turks and Poles, thus making them excellent for tracking the presence of Altaic admixture. In the new release, the Buryat modal haplotype that was previously found in a samples of Poles, has now been detected in a sample of Germans from Cologne.

June 17, 2005

A new study on human Y chromosomes has found a strong differentiation between German and Polish Y-chromosomes. The differentiation occurs precisely at the border between the two countries, with all German and all Polish populations clustering together.

The explanation for this phenomenon is that resettlements after WWII homogenized the two nations on an ethnic basis. Moreover, a necessary assumption is that there was little male admixture between the two peoples when they co-existed geographically.

The differentiation is evident based on analyses both of Y-STR haplotypes and Y-chromosomal haplogroups. The main contributors to the differentiation are the higher frequency of R1a1 in Poland and correspondingly higher frequency of R1*(xR1a1) in Germany, and the presence of different haplotype clusters for haplogroup I in the two countries. The correspondence analysis between haplogroups and populations is particularly interesting:

We see that Poles are differentiated by Germans on the basis of R1a1 and N3 (Finno-Ugrian admixture). The differentiation on the basis of I subgroups is not evident, because no downstream markers for this haplogroup were examined in this study.

Also of particular interest is that of the two Neolithic haplogroups, J2 is associated with Germans, whereas DE* is apparently not. So, this may hint at different patterns of arrival of the two haplogroups in this part of the world. This would agree with some recentresults from Balkan Slavic populations, that typically found a higher-percentage of YAP (DE) lineages than J2 ones.

Human Genetics (advanced publication online)

Significant genetic differentiation between Poland and Germany follows present-day political borders, as revealed by Y-chromosome analysis

Manfred Kayser et al.

Abstract To test for human population substructure and to investigate human population history we have analysed Y-chromosome diversity using seven microsatellites (Y-STRs) and ten binary markers (Y-SNPs) in samples from eight regionally distributed populations from Poland (n=913) and 11 from Germany (n=1,215). Based on data from both Y-chromosome marker systems, which we found to be highly correlated (r=0.96), and using spatial analysis of the molecular variance (SAMOVA), we revealed statistically significant support for two groups of populations: (1) all Polish populations and (2) all German populations. By means of analysis of the molecular variance (AMOVA) we observed a large and statistically significant proportion of 14% (for Y-SNPs) and 15% (for Y-STRs) of the respective total genetic variation being explained between both countries. The same population differentiation was detected using Monmonierrsquos algorithm, with a resulting genetic border between Poland and Germany that closely resembles the course of the political border between both countries. The observed genetic differentiation was mainly, but not exclusively, due to the frequency distribution of two Y-SNP haplogroups and their associated Y-STR haplotypes: R1a1*, most frequent in Poland, and R1*(xR1a1), most frequent in Germany. We suggest here that the pronounced population differentiation between the two geographically neighbouring countries, Poland and Germany, is the consequence of very recent events in human population history, namely the forced human resettlement of many millions of Germans and Poles during and, especially, shortly after World War II. In addition, our findings have consequences for the forensic application of Y-chromosome markers, strongly supporting the implementation of population substructure into forensic Y chromosome databases, and also for genetic association studies.

June 14, 2005

A new paper deals with the problem of whether or not men and women differ in intelligence, testing four proposed hypotheses:

The general conclusion: Proper methodology identifies a male advantage in g that increases exponentially at higher levels, relates to brain size, and explains, at least in part, the universal male dominance in society.

Personality and Individual Differences (Article in Press)

Sex-related differences in general intelligence g, brain size, and social status

Helmuth Nyborg

Abstract

The question of a sex difference in intelligence has long divided the experts. IQ researchers sum standardized subtest scores to calculate intelligence in general, and find that males outscore females by about 3.8 points, whereas factor analysts derive the g factor scores from intertest-correlations and find no consistent sex differences in general intelligence. The latter finding is puzzling, as males have larger average brains than females, and brain size correlates .30–.45 with g (and IQ). Males thus “ought” to score a higher g than females.

The present study addressed this paradox by testing four hypotheses: (1) Inadequate analyses explain why researchers get inconsistent results, (2) The proper method will identify a male g lead, (3) The larger male brain “explains” the male g lead, (4) The higher male g average and wider distribution transform into an exponentially increased male–female ratio at the high end of the g distribution, and this largely explains male dominance in society.

All four hypotheses obtained support and explain in part why relatively few males dominate the upper strata in all known societies. The confirmation of hypothesis 3 suggests that the brain size—intelligence–dominance link may be partly biological.

The extent and nature of SEE paternal genetic contribution to European genetic landscape was explored based on a high-resolution Y chromosome analysis involving 681 males from 7 populations in the region. Paternal lineages present in SEE were compared with previously published data from 81 western Eurasian populations and 5,017 Y chromosome samples. The finding that five major haplogroups (E3b1, I1b* (xM26), J2, R1a, R1b) comprise more than 70% of SEE total genetic variation is consistent with the typical European Y chromosome gene pool. However, distribution of major Y chromosomal lineages and estimated expansion signals clarify the specific role of this region in structuring of European, and particularly, Slavic paternal genetic heritage. Contemporary Slavic paternal gene pool, mostly characterized by the predominance of R1a and I1b* (xM26), and scarcity of E3b1 lineages, is a result of two major prehistoric gene flows with opposite directions: the post-LGM R1a expansion from east to west, the YD-Holocene I1b* (xM26) diffusion out of SEE in addition to subsequent R1a and I1b* (xM26) putative gene flows between eastern and southeastern Europe and a rather weak extent of E3b1 diffusion towards regions nowadays occupied by Slavic speaking populations.

June 10, 2005

A new paper indicates that Bronze Age cattle from Iberia already possessed some of the African haplotypes found in modern Iberian cattle. Therefore, cattle of African origin were introduced to Iberia before the Muslim invasion.

Proc Natl Acad Sci U S A. 2005 Jun 7; [Epub ahead of print]

Prehistoric contacts over the Straits of Gibraltar indicated by genetic analysis of Iberian Bronze Age cattle.

C. Anderung et al.

The geographic situation of the Iberian Peninsula makes it a natural link between Europe and North Africa. However, it is a matter of debate to what extent African influences via the Straits Gibraltar have affected Iberia's prehistoric development. Because early African pastoralist communities were dedicated to cattle breeding, a possible means to detect prehistoric African-Iberian contacts might be to analyze the origin of cattle breeds on the Iberian Peninsula. Some contemporary Iberian cattle breeds show a mtDNA haplotype, T1, that is characteristic to African breeds, generally explained as being the result of the Muslim expansion of the 8th century A.D., and of modern imports. To test a possible earlier African influence, we analyzed mtDNA of Bronze Age cattle from the Portalon cave at the Atapuerca site in northern Spain. Although the majority of samples showed the haplotype T3 that dominates among European breeds of today, the T1 haplotype was found in one specimen radiocarbon dated 1800 calibrated years B.C. Accepting T1 as being of African origin, this result indicates prehistoric African-Iberian contacts and lends support to archaeological finds linking early African and Iberian cultures. We also found a wild ox haplotype in the Iberian Bronze Age sample, reflecting local hybridization or backcrossing or that aurochs were hunted by these farming cultures.

June 08, 2005

I had previously posted about how Hammer et al. discovered a 2-million year old East Asian polymorphism, thus rejecting the pure Out of Africa model. Now, in a paper published in the journal Genetics they report a haplotype over a 17.5 kilobase sequence of the X chromosome where 2 out of 3 Mbuti (pygmoid) Africans have a haplotype that is over a million years old. Moreover, in the context of their statistical framework, the authors are able to reject the null hypothesis of "a single, historically panmictic population" originating in Africa.

These findings do not negate the fact that most human variation has a "shallow" time depth, but it is strong evidence that some humans have ancestry that is much more ancient than that of the bulk of mankind. In this case, the Mbuti pygmoids have apparently assimilated elements from archaic Africans.

This result may lend some support to my pet theory that the main differentiation in human genetic variation is between Paleoafricans who were reproductively isolated for a long time from the Afrasians, with subsequent hybridizaton between Afrasians and Paleoafricans in Africa. In this scheme, the Paleoafricans, perhaps descended from the earliest Homo sapiens population of East Africa picked up some pre-sapiens ancestry as they spread to the interior of Africa.

Fossil evidence links human ancestry with populations that evolved modern gracile morphology in Africa 130,000 - 160,000 years ago. Yet fossils alone do not provide clear answers to the question of whether the ancestors of all modern Homo sapiens comprised a single African population or an amalgamation of distinct archaic populations. DNA sequence data have consistently supported a single origin model in which anatomically modern Africans expanded and completely replaced all other archaic hominin populations. Aided by a novel experimental design, we present the first genetic evidence that statistically rejects the null hypothesis that our species descends from a single, historically panmictic population. In a global sample of 42 X chromosomes, two African individuals carry a lineage of non-coding 17.5 kilobase sequence that has survived for over one million years without any clear traces of ongoing recombination with other lineages at this locus. These patterns of deep haplotype divergence and long-range linkage disequilibrium are best explained by a prolonged period of ancestral population subdivision followed by relatively recent interbreeding. This inference supports human evolution models that incorporate admixture between divergent African branches of the genus Homo.

June 01, 2005

While the current distribution of lactase persistence in Eurasia and the African Fulbe seems to be due to the dispersion of a single mutation, it is still unclear what is the significance of the recent finding that –13910*T allele is absent from most African populations in which high frequencies of lactase persistence have been previously found with physiological tests (Mulcare et al. 2004).

Human Genetics (online first)

Microsatellite variation and evolution of human lactase persistence

Margarida Coelho et al.

Abstract The levels of haplotype diversity within the lineages defined by two single-nucleotide polymorphisms (SNPs) (–13910 C/T and –22018 G/A) associated with human lactase persistence were assessed with four fast-evolving microsatellite loci in 794 chromosomes from Portugal, Italy, Fulbe from Cameroon, São Tomé and Mozambique. Age estimates based on the intraallelic microsatellite variation indicate that the –13910*T allele, which is more tightly associated with lactase persistence, originated in Eurasia before the Neolithic and after the emergence of modern humans outside Africa. We detected significant departures from neutrality for the –13910*T variant in geographically and evolutionary distant populations from southern Europe (Portuguese and Italians) and Africa (Fulbe) by using a neutrality test based on the congruence between the frequency of the allele and the levels of intraallelic variability measured by the number of mutations in adjacent microsatellites. This result supports the role of selection in the evolution of lactase persistence, ruling out possible confounding effects from recombination suppression and population history. Reevaluation of the available evidence on variation of the –13910 and –22018 loci indicates that lactase persistence probably originated from different mutations in Europe and most of Africa, even if 13910*T is not the causal allele, suggesting that selective pressure could have promoted the convergent evolution of the trait. Our study shows that a limited number of microsatellite loci may provide sufficient resolution to reconstruct key aspects of the evolutionary history of lactase persistence, providing an alternative to approaches based on large numbers of SNPs.

Related to my previous post on mtDNA and the western Bantu expansion, a new article investigates the process of the spread of the western Bantu languages, which was associated with a complete replacement of earlier hunter-gatherer Y chromosomes, as well as other event.

Human Genetics (online first)

The genetic legacy of western Bantu migrations

Sandra Beleza et al.

Abstract There is little knowledge on the demographic impact of the western wave of the Bantu expansion. Only some predictions could be made based mainly on indirect archaeological, linguistic, and genetic evidences. Apart from the very limited available data on the mitochondrial DNA (mtDNA) side, there are not, however, Y-chromosome studies revealing–if any–the male contribution of western Bantu-farmers. To elucidate the still poorly characterized western Bantu expansion, we analyzed Y-chromosome (25 biallelic polymorphisms and 15 microsatellite markers) and mtDNA (hypervariable control regions I and II and selected coding region RFLPs) variation in a population of 110 individuals from southwest Africa, and compared it with a database of 2,708 Y-chromosome profiles and of 2,565 mtDNAs from all other regions of Africa. This study reveals (1) a dramatic displacement of male and female Khoisan-speaking groups in the southwest, since both the maternal and the paternal genetic pools were composed exclusively by types carried by Bantu-speakers; (2) a clear bias in the admixture process towards the mating of male Europeans with female Sub-Saharan Africans; (3) the assimilation of east African lineages by the southwest (mainly mtDNA-L3f and Y-chromosome-B2a lineages); and (4) signatures of recent male and female gene flow from the southeast into the southwest. The data also indicate that the western stream of the Bantu expansion was a more gradual process than the eastern counterpart, which likely involved multiple short dispersals.

Analysis of the maize genome, indicates that its domestication resulted in a population bottleneck, resulting in loss of genetic diversity, and also artificial selection on several genes, apparently due to the action of humans.

Science, Vol 308, Issue 5726, 1310-1314 , 27 May 2005

The Effects of Artificial Selection on the Maize Genome

Stephen I. Wright et al.

Domestication promotes rapid phenotypic evolution through artificial selection. We investigated the genetic history by which the wild grass teosinte (Zea mays ssp. parviglumis) was domesticated into modern maize (Z. mays ssp. mays). Analysis of single-nucleotide polymorphisms in 774 genes indicates that 2 to 4% of these genes experienced artificial selection. The remaining genes retain evidence of a population bottleneck associated with domestication. Candidate selected genes with putative function in plant growth are clustered near quantitative trait loci that contribute to phenotypic differences between maize and teosinte. If we assume that our sample of genes is representative, ~1200 genes throughout the maize genome have been affected by artificial selection.

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